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I am not sure how he made this website.. I basically just copied and pasted the html code
I suspect that is your major problem.
The correct way to do it is to open up the REMOTE website and PUBLISH is back to your computer. Just make an empty website on your computer, then publish it that.
2. The sidebar could have been done using CSS or a div placing it on a certain location on the page (wild guess).
3. It does matter how you upload the site. There are several features of Frontpage that get messed up if you FTP it. General advice when using FP is to publish the site to be on the safe side.
4. If you are starting a new sidebar investigate FP "includes" or Server Side Includes to save yourself a lot of trouble updating it in future.